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Kindlegen puts two files in the output mobi - a KF8 format file for devices which can use those features and a conventional mobi for older devices.

When you say there is no TOC, did you mean the html TOC or the NCX navigational TOC (the one that works with the four-way controller button on some kindles)?

Also the server side on Amazon post-processes the mobi file from kindlegen. You should always download the converted file from KDP BEFORE the book goes live. You have this option before you continue on the various menus after it says the file has been uploaded and properly converted. Do this even for an uploaded mobi file. 

I also keep one book always in draft, just for checking uploaded files. The purpose of that book is to simply check the Amazon post-processing of the uploaded file.
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